Jul 20, 2023

Alignment tools for the structural analysis of RNA

The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction the minimum free energy algorithm of Zuker & Stiegler 1981 which yields a single optimal structure, the partition function algorithm of McCaskill 1990 which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of Wuchty 1999 which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance dissimilarities using either string alignment or tree-editing Shapiro & Zhang 1990. Finally, we provide an algorithm to design sequences with a predefined structure inverse folding.

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